Training Meeting
Microme
–
Marseilles
-
28/03/2012.
David
Vallenet
, François
Le
Fèvre
, Damien
Mornico
,
Maria Jose Lopez, Eugenio
Belda
,
Claudine
Médigue
Web Service
Dedicated
to Metabolism
Laboratory of Bioinformatic Analysis in Genomic and Metabolism (LABGeM team)
CEA/DSV/IG/Genoscope & CNRS UMR8030
Some of
the
Microme
‘s needs
Data Retrieval
•
Specific
•
Dump of data
Services
•
exposition of expert methods
(read access)
•
integration of expert methods
(write access)
WEB SERVICE
3/30/2012
CEA / LABGeM partner
-
Microme Training
2
CEA Accessible Data / Information
Compound :
Chebi
Reaction : Rhea
GPR : MicroScope
Pathway: Microscope
Genomic : Microscope
Phenotype: Microscope
PREDICTED
& EXPERT
CURATION
3/30/2012
CEA / LABGeM partner
-
Microme Training
3
Web service to retrieve the Gene Protein Relationship
3/30/2012
CEA / LABGeM partner
-
Microme Training
4
Metabolic workflow
Data retrieval layer
Application design
Model insight
Available services
Analyzing results
Metabolic Workflow
pkgdb
MicroCyc
PGDB
MicroDb
PathoLogic
Formatter
Complexes
Generator
MicroDB
Generator
Expert validation
Automatic pipeline
3/30/2012
CEA / LABGeM partner
-
Microme Training
5
Data Retrieval Layer
MicroDb
Web Service
MicroScope
MicroCyc Web
PkGDB
MicroScope
3/30/2012
CEA / LABGeM partner
-
Microme Training
6
Application Design
UML specification
Automatic generation
Back end
Persistence
Entity
Services
Technologies
Java (Hibernate/Spring)
Maven
AndroMDA
http://www.andromda.org/docs/index.html
3/30/2012
CEA / LABGeM partner
-
Microme Training
7
From PGDB to reaction
3/30/2012
CEA / LABGeM partner
-
Microme Training
8
Gene Protein Relationship
3/30/2012
CEA / LABGeM partner
-
Microme Training
9
Protein Reaction Relationship
3/30/2012
CEA / LABGeM partner
-
Microme Training
10
Available Service 1.0
3/30/2012
CEA / LABGeM partner
-
Microme Training
11
Accessible Genomes
Hamap
code
Microscope id
BioCyc
version
3/30/2012
CEA / LABGeM partner
-
Microme Training
12
Gene Details
Id MicroScope
Id MicroCyc
Id
UniProt
Id
RefSeq
Evidence Genomic
•
Automatic: Transfert of annotation
•
Validated: Human Expert Curation
3/30/2012
CEA / LABGeM partner
-
Microme Training
13
Complex Encoding
<
ns:gprSimpleVO
xsi:type
="
ns:GprSimpleVO
">
<
ns:associatedGenes
>
<
ns:geneSimpleVO
xsi:type
="
ns:GeneSimpleVO
">
<ns:accession1>GO145023</ns:accession1>
<
ns:frame
>G2NI
-
1492</
ns:frame
>
<
ns:id
>14363</
ns:id
>
<
ns:shortName
>
linC
</
ns:shortName
>
</
ns:geneSimpleVO
>
<
ns:geneSimpleVO
xsi:type
="
ns:GeneSimpleVO
">
<
ns:accession1>GO145024</
ns:accession1>
<
ns:frame
>G2NI
-
1493</
ns:frame
>
<
ns:id
>14364</
ns:id
>
<
ns:shortName
>
linD
</
ns:shortName
>
</
ns:geneSimpleVO
>
</
ns:associatedGenes
>
<
ns:catalyzedReactionCommonName
>ACIAD1575_linCD</
ns:catalyzedReact
ionCommonName
>
<
ns:ecNumber
>1.14.99.28</
ns:ecNumber
>
<
ns:frameReaction
>LINALOOL
-
8
-
MONOOXYGENASE
-
RXN</
ns:frameReaction
>
<
ns:gpr
>G2NI
-
1492</
ns:gpr
>
<
ns:gprEvidence
>
validated
</
ns:gprEvidence
>
<
ns:reactionCommonName
>
linalool
8
-
monooxygenase</
ns:reactionCommonName
>
</
ns:gprSimpleVO
>
GO145023
GO145024
RXN0
-
2606
Id MicroCyc
G(P)R
Evidence
3/30/2012
CEA / LABGeM partner
-
Microme Training
14
Isozyme
Encoding or putative Complex?
<
ns:gprSimpleVO
xsi:type
="
ns:GprSimpleVO
">
<
ns:ecNumber
>NIL</
ns:ecNumber
>
<
ns:frameReaction
>DISULFOXRED
-
RXN</
ns:frameReaction
>
<
ns:gpr
>GEL
-
4936@EB7Av1_1080005_dsbA$GO3290285</
ns:gpr
>
<
ns:gprEvidence
>
predicted
</
ns:gprEvid
ence
>
</
ns:gprSimpleVO
>
<
ns:gprSimpleVO
xsi:type
="
ns:GprSimpleVO
">
<
ns:ecNumber
>NIL</
ns:ecNumber
>
<
ns:frameReaction
>DISULFOXRED
-
RXN</
ns:frameReaction
>
<
ns:gpr
>GEL
-
1163@EB7Av1_90089_dsbC$GO3286552</
ns:gpr
>
<
ns:gprEvidence
>
predicted
</
ns:gprEvid
ence
>
</
ns:gprSimpleVO
>
<
ns:gprSimpleVO
xsi:type
="
ns:GprSimpleVO
">
<
ns:ecNumber
>NIL</
ns:ecNumber
>
<
ns:frameReaction
>DISULFOXRED
-
RXN</
ns:frameReaction
>
<
ns:gpr
>GEL
-
2576@EB7Av1_290029_dsbG$GO3287959</
ns:gpr
>
<
ns:gprEvidence
>
predicted
</
ns:gprEvid
ence
>
</
ns:gprSimpleVO
>
GO3290285
GO3286552
GO3286297
DISULFOXRED
-
RXN
GO3290285
GO3286552
GO3286297
DISULFOXRED
-
RXN
3/30/2012
CEA / LABGeM partner
-
Microme Training
15
Storing and managing growth phenotype
3/30/2012
CEA / LABGeM partner
-
Microme Training
16
Growth phenotype
Model proposition
Growth phenotype
Objective
•
Store the result of growth phenotype experiment
•
Query methods
•
Relationship with genomic annotation
•
Relationship with models
Difficulties
•
What is a growth phenotype results (0
-
1 ?)
•
How to manage replicates ?
•
How to integrate expert curation ?
•
How to interpolate result ? (0
-
1
auxotrophy)
3/30/2012
CEA / LABGeM partner
-
Microme Training
17
Experiment
3/30/2012
CEA / LABGeM partner
-
Microme Training
18
Growth Phenotype
3/30/2012
CEA / LABGeM partner
-
Microme Training
19
Medium
3/30/2012
CEA / LABGeM partner
-
Microme Training
20
Strain
3/30/2012
CEA / LABGeM partner
-
Microme Training
21
3/30/2012
CEA / LABGeM partner
-
Microme Training
22
Other projects
Outlook
Training
Other projects in development
3/30/2012
CEA / LABGeM partner
-
Microme Training
23
Main Entry point
http://www.genoscope.cns.fr/microme/
3/30/2012
CEA / LABGeM partner
-
Microme Training
24
Interactions Outlook &
Open Questions
W
e
b
S
e
r
v
i
c
e
MicroScope
WebService
/ UI / Web
GPRs
Microme
Update
Frequency?
Integration
Process ?
Partner
Tools
CEATools
Integration
Process ?
3/30/2012
CEA / LABGeM partner
-
Microme Training
25
Training with
webservice
Generation
of java
client
Query
several
webservices
Manipulate
the data
3/30/2012
CEA / LABGeM partner
-
Microme Training
26
Thanks for Interaction
ULB partner
Jacques van
Helden
Didier
Croes
Quentin
Dacosta
Jonathan
Verneau
CERTH partner
Christos
Ouzounis
Fotis
Psomopoulos
3/30/2012
CEA / LABGeM partner
-
Microme Training
27
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